@article {214,
	title = {De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation},
	journal = {Nucleic Acids Research},
	volume = {44},
	year = {2016},
	month = {04/2016},
	pages = {3013-3019},
	chapter = {3013},
	abstract = {<p>The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, biomolecular medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate <em>de novo</em> reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures.</p>
},
	doi = {10.1093/nar/gkw155},
	url = {http://nar.oxfordjournals.org/content/early/2016/03/14/nar.gkw155},
	author = {Christopher Maffeo and Jejoong Yoo and Aleksei Aksimentiev}
}
